@gmod/bbi 7.0.5 → 8.0.0

package/CHANGELOG.md

@@ -1,3 +1,11 @@
+# [8.0.0](https://github.com/GMOD/bbi-js/compare/v7.1.0...v8.0.0) (2025-12-11)
+
+
+
+# [7.1.0](https://github.com/GMOD/bbi-js/compare/v7.0.5...v7.1.0) (2025-11-09)
+
+
+
 ## [7.0.5](https://github.com/GMOD/bbi-js/compare/v7.0.4...v7.0.5) (2025-06-10)
 
 

package/README.md

@@ -123,6 +123,65 @@ observer.subscribe(
 )
 ```
 
+#### getFeaturesAsArrays(refName, start, end, opts)
+
+Same parameters as getFeatures, but returns typed arrays instead of an array of
+objects. This is more memory-efficient and reduces garbage collection pressure
+for large datasets.
+
+```typescript
+const result = await bigwig.getFeaturesAsArrays('chr1', 0, 100000)
+// For regular BigWig data:
+// { starts: Int32Array, ends: Int32Array, scores: Float32Array }
+
+// For summary/zoomed data (when using scale parameter):
+// { starts: Int32Array, ends: Int32Array, scores: Float32Array,
+//   minScores: Float32Array, maxScores: Float32Array }
+```
+
+Example usage:
+
+```typescript
+const { starts, ends, scores } = await bigwig.getFeaturesAsArrays(
+  'chr1',
+  0,
+  100000,
+)
+for (let i = 0; i < starts.length; i++) {
+  console.log(`Feature at ${starts[i]}-${ends[i]} with score ${scores[i]}`)
+}
+
+// Check if it's summary data
+const result = await bigwig.getFeaturesAsArrays('chr1', 0, 100000, {
+  scale: 0.01,
+})
+if ('minScores' in result) {
+  // Summary data with min/max scores
+  const { minScores, maxScores } = result
+  for (let i = 0; i < starts.length; i++) {
+    console.log(`Range: ${minScores[i]} - ${maxScores[i]}`)
+  }
+}
+```
+
+TypeScript types:
+
+```typescript
+interface BigWigFeatureArrays {
+  starts: Int32Array
+  ends: Int32Array
+  scores: Float32Array
+}
+
+interface SummaryFeatureArrays {
+  starts: Int32Array
+  ends: Int32Array
+  scores: Float32Array
+  minScores: Float32Array
+  maxScores: Float32Array
+}
+```
+
 ### BigBed
 
 #### getFeatures(refName, start, end, opts)

package/dist/bbi.d.ts

@@ -1,6 +1,6 @@
 import { Observable } from 'rxjs';
 import { BlockView } from './block-view.ts';
-import type { BigWigHeaderWithRefNames, Feature, RequestOptions2, RequestOptions } from './types.ts';
+import type { BigWigFeatureArrays, BigWigHeaderWithRefNames, Feature, RequestOptions2, RequestOptions, SummaryFeatureArrays } from './types.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 export declare abstract class BBI {
     protected bbi: GenericFilehandle;
@@ -15,7 +15,7 @@ export declare abstract class BBI {
     });
     private _getHeader;
     private _getMainHeader;
-    private _readChromTree;
+    private _readChromosomeTree;
     protected getUnzoomedView(opts?: RequestOptions): Promise<BlockView>;
     protected abstract getView(scale: number, opts?: RequestOptions): Promise<BlockView>;
     /**
@@ -31,5 +31,15 @@ export declare abstract class BBI {
      * or scale used to infer the zoomLevel to use
      */
     getFeatureStream(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<Observable<Feature[]>>;
-    getFeatures(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<Feature[]>;
+    getFeatures(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<any[]>;
+    /**
+     * Gets features from a BigWig file as typed arrays (more efficient than getFeatures)
+     *
+     * @param refName - The chromosome name
+     * @param start - The start of a region
+     * @param end - The end of a region
+     * @param opts - Options including basesPerSpan or scale
+     * @returns Promise with typed arrays: starts, ends, scores (and minScores/maxScores for summary data)
+     */
+    getFeaturesAsArrays(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<BigWigFeatureArrays | SummaryFeatureArrays>;
 }

package/dist/bbi.js

@@ -7,10 +7,14 @@ const operators_1 = require("rxjs/operators");
 const block_view_ts_1 = require("./block-view.js");
 const BIG_WIG_MAGIC = -2003829722;
 const BIG_BED_MAGIC = -2021002517;
+const decoder = new TextDecoder('utf8');
 function getDataView(buffer) {
     return new DataView(buffer.buffer, buffer.byteOffset, buffer.length);
 }
 class BBI {
+    bbi;
+    headerP;
+    renameRefSeqs;
     getHeader(opts) {
         if (!this.headerP) {
             this.headerP = this._getHeader(opts).catch((e) => {
@@ -48,7 +52,7 @@ class BBI {
     }
     async _getHeader(opts) {
         const header = await this._getMainHeader(opts);
-        const chroms = await this._readChromTree(header, opts);
+        const chroms = await this._readChromosomeTree(header, opts);
         return {
             ...header,
             ...chroms,
@@ -68,7 +72,8 @@ class BBI {
         offset += 2;
         const numZoomLevels = dataView.getUint16(offset, true);
         offset += 2;
-        const chromTreeOffset = Number(dataView.getBigUint64(offset, true));
+        // Offset to the B+ tree that maps chromosome names to integer IDs
+        const chromosomeTreeOffset = Number(dataView.getBigUint64(offset, true));
         offset += 8;
         const unzoomedDataOffset = Number(dataView.getBigUint64(offset, true));
         offset += 8;
@@ -111,7 +116,7 @@ class BBI {
         }
         let totalSummary;
         if (totalSummaryOffset) {
-            const b2 = b.subarray(Number(totalSummaryOffset));
+            const b2 = b.subarray(totalSummaryOffset);
             let offset = 0;
             const dataView = getDataView(b2);
             const basesCovered = Number(dataView.getBigUint64(offset, true));
@@ -135,7 +140,6 @@ class BBI {
         else {
             throw new Error('no stats');
         }
-        const decoder = new TextDecoder('utf8');
         return {
             zoomLevels,
             magic,
@@ -146,7 +150,7 @@ class BBI {
             definedFieldCount,
             uncompressBufSize,
             asOffset,
-            chromTreeOffset,
+            chromosomeTreeOffset,
             totalSummaryOffset,
             unzoomedDataOffset,
             unzoomedIndexOffset,
@@ -157,11 +161,14 @@ class BBI {
                 : '',
         };
     }
-    async _readChromTree(header, opts) {
+    // Reads the B+ tree that maps chromosome names to integer IDs
+    // This is part of the "cirTree" (combined ID R-tree) structure, which uses
+    // integer chromosome IDs instead of strings for more efficient spatial indexing
+    async _readChromosomeTree(header, opts) {
         const refsByNumber = [];
         const refsByName = {};
-        const chromTreeOffset = Number(header.chromTreeOffset);
-        const dataView = getDataView(await this.bbi.read(32, chromTreeOffset, opts));
+        const chromosomeTreeOffset = header.chromosomeTreeOffset;
+        const dataView = getDataView(await this.bbi.read(32, chromosomeTreeOffset, opts));
         let offset = 0;
         // const magic = dataView.getUint32(offset, true) // unused
         offset += 4;
@@ -173,8 +180,8 @@ class BBI {
         offset += 4;
         // const itemCount = dataView.getBigUint64(offset, true) // unused
         offset += 8;
-        const decoder = new TextDecoder('utf8');
-        const bptReadNode = async (currentOffset) => {
+        // Recursively traverses the B+ tree to populate chromosome name-to-ID mappings
+        const readBPlusTreeNode = async (currentOffset) => {
             const b = await this.bbi.read(4, currentOffset);
             const dataView = getDataView(b);
             let offset = 0;
@@ -184,14 +191,14 @@ class BBI {
             offset += 1;
             const count = dataView.getUint16(offset, true);
             offset += 2;
+            // Leaf nodes contain the actual chromosome name-to-ID mappings
             if (isLeafNode) {
                 const b = await this.bbi.read(count * (keySize + valSize), currentOffset + offset);
                 const dataView = getDataView(b);
                 offset = 0;
                 for (let n = 0; n < count; n++) {
-                    const key = decoder
-                        .decode(b.subarray(offset, offset + keySize))
-                        .replaceAll('\0', '');
+                    const keyEnd = b.indexOf(0, offset);
+                    const key = decoder.decode(b.subarray(offset, keyEnd !== -1 ? keyEnd : offset + keySize));
                     offset += keySize;
                     const refId = dataView.getUint32(offset, true);
                     offset += 4;
@@ -206,6 +213,7 @@ class BBI {
                 }
             }
             else {
+                // Non-leaf nodes contain pointers to child nodes
                 const nextNodes = [];
                 const dataView = getDataView(await this.bbi.read(count * (keySize + 8), currentOffset + offset));
                 offset = 0;
@@ -213,12 +221,12 @@ class BBI {
                     offset += keySize;
                     const childOffset = Number(dataView.getBigUint64(offset, true));
                     offset += 8;
-                    nextNodes.push(bptReadNode(childOffset));
+                    nextNodes.push(readBPlusTreeNode(childOffset));
                 }
                 await Promise.all(nextNodes);
             }
         };
-        await bptReadNode(chromTreeOffset + 32);
+        await readBPlusTreeNode(chromosomeTreeOffset + 32);
         return {
             refsByName,
             refsByNumber,
@@ -230,7 +238,7 @@ class BBI {
      */
     async getUnzoomedView(opts) {
         const { unzoomedIndexOffset, refsByName, uncompressBufSize, fileType } = await this.getHeader(opts);
-        return new block_view_ts_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, uncompressBufSize > 0, fileType);
+        return new block_view_ts_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, uncompressBufSize, fileType);
     }
     /**
      * Gets features from a BigWig file
@@ -268,8 +276,63 @@ class BBI {
     }
     async getFeatures(refName, start, end, opts) {
         const ob = await this.getFeatureStream(refName, start, end, opts);
-        const ret = await (0, rxjs_1.firstValueFrom)(ob.pipe((0, operators_1.toArray)()));
-        return ret.flat();
+        const arrays = await (0, rxjs_1.firstValueFrom)(ob.pipe((0, operators_1.toArray)()));
+        const totalLength = arrays.reduce((sum, arr) => sum + arr.length, 0);
+        const result = new Array(totalLength);
+        let index = 0;
+        for (const arr of arrays) {
+            for (const item of arr) {
+                result[index++] = item;
+            }
+        }
+        return result;
+    }
+    /**
+     * Gets features from a BigWig file as typed arrays (more efficient than getFeatures)
+     *
+     * @param refName - The chromosome name
+     * @param start - The start of a region
+     * @param end - The end of a region
+     * @param opts - Options including basesPerSpan or scale
+     * @returns Promise with typed arrays: starts, ends, scores (and minScores/maxScores for summary data)
+     */
+    async getFeaturesAsArrays(refName, start, end, opts) {
+        const features = await this.getFeatures(refName, start, end, opts);
+        const count = features.length;
+        if (count === 0) {
+            return {
+                starts: new Int32Array(0),
+                ends: new Int32Array(0),
+                scores: new Float32Array(0),
+            };
+        }
+        const hasSummary = features[0]?.summary === true;
+        if (hasSummary) {
+            const starts = new Int32Array(count);
+            const ends = new Int32Array(count);
+            const scores = new Float32Array(count);
+            const minScores = new Float32Array(count);
+            const maxScores = new Float32Array(count);
+            for (let i = 0; i < count; i++) {
+                const f = features[i];
+                starts[i] = f.start;
+                ends[i] = f.end;
+                scores[i] = f.score ?? 0;
+                minScores[i] = f.minScore ?? 0;
+                maxScores[i] = f.maxScore ?? 0;
+            }
+            return { starts, ends, scores, minScores, maxScores };
+        }
+        const starts = new Int32Array(count);
+        const ends = new Int32Array(count);
+        const scores = new Float32Array(count);
+        for (let i = 0; i < count; i++) {
+            const f = features[i];
+            starts[i] = f.start;
+            ends[i] = f.end;
+            scores[i] = f.score ?? 0;
+        }
+        return { starts, ends, scores };
     }
 }
 exports.BBI = BBI;

package/dist/bbi.js.map

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package/dist/bigbed.d.ts

@@ -1,6 +1,6 @@
 import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 import { BBI } from './bbi.ts';
-import type { Feature, RequestOptions } from './types.ts';
+import type { RequestOptions } from './types.ts';
 interface Index {
     type: number;
     fieldcount: number;
@@ -14,6 +14,18 @@ export declare class BigBed extends BBI {
     protected getView(_scale: number, opts?: RequestOptions): Promise<import("./block-view.ts").BlockView>;
     private _readIndices;
     private searchExtraIndexBlocks;
-    searchExtraIndex(name: string, opts?: RequestOptions): Promise<Feature[]>;
+    searchExtraIndex(name: string, opts?: RequestOptions): Promise<{
+        field: number | undefined;
+        offset?: number;
+        chromId?: number;
+        start: number;
+        end: number;
+        score?: number;
+        rest?: string;
+        minScore?: number;
+        maxScore?: number;
+        summary?: boolean;
+        uniqueId?: string;
+    }[]>;
 }
 export {};

package/dist/bigbed.js

@@ -10,17 +10,113 @@ const quick_lru_1 = __importDefault(require("quick-lru"));
 const rxjs_1 = require("rxjs");
 const operators_1 = require("rxjs/operators");
 const bbi_ts_1 = require("./bbi.js");
+const decoder = new TextDecoder('utf8');
 function filterUndef(ts) {
     return ts.filter((t) => !!t);
 }
-class BigBed extends bbi_ts_1.BBI {
-    constructor() {
-        super(...arguments);
-        this.readIndicesCache = new abortable_promise_cache_1.default({
-            cache: new quick_lru_1.default({ maxSize: 1 }),
-            fill: (args, signal) => this._readIndices({ ...args, signal }),
-        });
+function getTabField(str, fieldIndex) {
+    if (fieldIndex < 0) {
+        return undefined;
+    }
+    let start = 0;
+    for (let i = 0; i < fieldIndex; i++) {
+        start = str.indexOf('\t', start);
+        if (start === -1) {
+            return undefined;
+        }
+        start++;
+    }
+    const end = str.indexOf('\t', start);
+    return end === -1 ? str.slice(start) : str.slice(start, end);
+}
+// Parses a null-terminated string key from a B+ tree node
+function parseKey(buffer, offset, keySize) {
+    const keyEnd = buffer.indexOf(0, offset);
+    return decoder.decode(buffer.subarray(offset, keyEnd !== -1 ? keyEnd : offset + keySize));
+}
+// Recursively traverses a B+ tree to search for a specific name in the BigBed extraIndex
+// B+ trees are balanced tree structures optimized for disk-based searches
+async function readBPlusTreeNode(bbi, nodeOffset, blockSize, keySize, valSize, name, field, opts) {
+    const len = 4 + blockSize * (keySize + valSize);
+    const buffer = await bbi.read(len, nodeOffset, opts);
+    const dataView = new DataView(buffer.buffer, buffer.byteOffset, buffer.length);
+    let offset = 0;
+    const nodeType = dataView.getInt8(offset);
+    offset += 2; // skip nodeType byte + 1 reserved byte
+    const cnt = dataView.getInt16(offset, true);
+    offset += 2;
+    // Non-leaf node (nodeType === 0): contains keys and child node pointers for navigation
+    if (nodeType === 0) {
+        const leafkeys = [];
+        for (let i = 0; i < cnt; i++) {
+            const key = parseKey(buffer, offset, keySize);
+            offset += keySize;
+            const dataOffset = Number(dataView.getBigUint64(offset, true));
+            offset += 8;
+            leafkeys.push({
+                key,
+                offset: dataOffset,
+            });
+        }
+        // Binary search to find the appropriate child node
+        let left = 0;
+        let right = leafkeys.length - 1;
+        let targetIndex = leafkeys.length - 1;
+        while (left <= right) {
+            const mid = Math.floor((left + right) / 2);
+            const cmp = name.localeCompare(leafkeys[mid].key);
+            if (cmp < 0) {
+                targetIndex = mid - 1;
+                right = mid - 1;
+            }
+            else {
+                left = mid + 1;
+            }
+        }
+        const childOffset = targetIndex >= 0 ? leafkeys[targetIndex].offset : leafkeys[0].offset;
+        return readBPlusTreeNode(bbi, childOffset, blockSize, keySize, valSize, name, field, opts);
+    }
+    else if (nodeType === 1) {
+        // Leaf node (nodeType === 1): contains actual key-value data
+        const keys = [];
+        for (let i = 0; i < cnt; i++) {
+            const key = parseKey(buffer, offset, keySize);
+            offset += keySize;
+            const dataOffset = Number(dataView.getBigUint64(offset, true));
+            offset += 8;
+            const length = dataView.getUint32(offset, true);
+            offset += 4;
+            offset += 4; // skip reserved
+            keys.push({
+                key,
+                offset: dataOffset,
+                length,
+            });
+        }
+        // Binary search for exact key match in sorted leaf node
+        let left = 0;
+        let right = keys.length - 1;
+        while (left <= right) {
+            const mid = Math.floor((left + right) / 2);
+            const cmp = name.localeCompare(keys[mid].key);
+            if (cmp === 0) {
+                return { ...keys[mid], field };
+            }
+            else if (cmp < 0) {
+                right = mid - 1;
+            }
+            else {
+                left = mid + 1;
+            }
+        }
+        return undefined;
     }
+}
+class BigBed extends bbi_ts_1.BBI {
+    readIndicesCache = new abortable_promise_cache_1.default({
+        cache: new quick_lru_1.default({ maxSize: 1 }),
+        fill: (args, signal) => this._readIndices({ ...args, signal }),
+    });
     readIndices(opts = {}) {
         const { signal, ...rest } = opts;
         return this.readIndicesCache.get(JSON.stringify(rest), opts, signal);
@@ -40,7 +136,7 @@ class BigBed extends bbi_ts_1.BBI {
      */
     async _readIndices(opts) {
         const { extHeaderOffset } = await this.getHeader(opts);
-        const b = await this.bbi.read(64, Number(extHeaderOffset));
+        const b = await this.bbi.read(64, extHeaderOffset);
         const dataView = new DataView(b.buffer, b.byteOffset, b.length);
         let offset = 0;
         // const _size = dataView.getUint16(offset, true)
@@ -55,7 +151,7 @@ class BigBed extends bbi_ts_1.BBI {
         }
         const blocklen = 20;
         const len = blocklen * count;
-        const buffer = await this.bbi.read(len, Number(dataOffset));
+        const buffer = await this.bbi.read(len, dataOffset);
         const indices = [];
         for (let i = 0; i < count; i += 1) {
             const b = buffer.subarray(i * blocklen);
@@ -66,9 +162,14 @@ class BigBed extends bbi_ts_1.BBI {
             const fieldcount = dataView.getInt16(offset, true);
             offset += 2;
             const dataOffset = Number(dataView.getBigUint64(offset, true));
-            offset += 8 + 4; //4 skip
+            offset += 8 + 4; // skip 8-byte offset + 4 reserved bytes
             const field = dataView.getInt16(offset, true);
-            indices.push({ type, fieldcount, offset: Number(dataOffset), field });
+            indices.push({
+                type,
+                fieldcount,
+                offset: dataOffset,
+                field,
+            });
         }
         return indices;
     }
@@ -87,7 +188,6 @@ class BigBed extends bbi_ts_1.BBI {
         if (indices.length === 0) {
             return [];
         }
-        const decoder = new TextDecoder('utf8');
         const locs = indices.map(async (index) => {
             const { offset: offset2, field } = index;
             const b = await this.bbi.read(32, offset2, opts);
@@ -103,72 +203,7 @@ class BigBed extends bbi_ts_1.BBI {
             offset += 4;
             // const _itemCount = Number(dataView.getBigUint64(offset, true))
             offset += 8;
-            const bptReadNode = async (nodeOffset) => {
-                const val = Number(nodeOffset);
-                const len = 4 + blockSize * (keySize + valSize);
-                const buffer = await this.bbi.read(len, val, opts);
-                const b = buffer;
-                const dataView = new DataView(b.buffer, b.byteOffset, b.length);
-                let offset = 0;
-                const nodeType = dataView.getInt8(offset);
-                offset += 2; //skip 1
-                const cnt = dataView.getInt16(offset, true);
-                offset += 2;
-                const keys = [];
-                if (nodeType === 0) {
-                    const leafkeys = [];
-                    for (let i = 0; i < cnt; i++) {
-                        const key = decoder
-                            .decode(b.subarray(offset, offset + keySize))
-                            .replaceAll('\0', '');
-                        offset += keySize;
-                        const dataOffset = Number(dataView.getBigUint64(offset, true));
-                        offset += 8;
-                        leafkeys.push({
-                            key,
-                            offset: dataOffset,
-                        });
-                    }
-                    let lastOffset = 0;
-                    for (const { key, offset } of leafkeys) {
-                        if (name.localeCompare(key) < 0 && lastOffset) {
-                            return bptReadNode(lastOffset);
-                        }
-                        lastOffset = offset;
-                    }
-                    return bptReadNode(lastOffset);
-                }
-                else if (nodeType === 1) {
-                    for (let i = 0; i < cnt; i++) {
-                        const key = decoder
-                            .decode(b.subarray(offset, offset + keySize))
-                            .replaceAll('\0', '');
-                        offset += keySize;
-                        const dataOffset = Number(dataView.getBigUint64(offset, true));
-                        offset += 8;
-                        const length = dataView.getUint32(offset, true);
-                        offset += 4;
-                        const reserved = dataView.getUint32(offset, true);
-                        offset += 4;
-                        keys.push({
-                            key,
-                            offset: dataOffset,
-                            length,
-                            reserved,
-                        });
-                    }
-                    for (const n of keys) {
-                        if (n.key === name) {
-                            return {
-                                ...n,
-                                field,
-                            };
-                        }
-                    }
-                    return undefined;
-                }
-            };
-            return bptReadNode(offset2 + 32);
+            return readBPlusTreeNode(this.bbi, offset2 + 32, blockSize, keySize, valSize, name, field, opts);
         });
         return filterUndef(await Promise.all(locs));
     }
@@ -179,7 +214,7 @@ class BigBed extends bbi_ts_1.BBI {
      *
      * @param name - the name to search for
      *
-     * @param opts - options object with optional AboutSignal
+     * @param opts - options object with optional AbortSignal
      *
      * @return array of Feature
      */
@@ -194,15 +229,21 @@ class BigBed extends bbi_ts_1.BBI {
                 view.readFeatures(observer, [block], opts).catch((e) => {
                     observer.error(e);
                 });
-            }).pipe((0, operators_1.reduce)((acc, curr) => acc.concat(curr)), (0, operators_1.map)(x => {
-                for (const element of x) {
-                    element.field = block.field;
-                }
-                return x;
-            }));
+            }).pipe((0, operators_1.reduce)((acc, curr) => {
+                acc.push(...curr);
+                return acc;
+            }, []), (0, operators_1.map)(features => features.map(f => ({ ...f, field: block.field }))));
         });
         const ret = await (0, rxjs_1.firstValueFrom)((0, rxjs_1.merge)(...res));
-        return ret.filter(f => f.rest?.split('\t')[(f.field || 0) - 3] === name);
+        // Filter to features where the indexed field matches the search name
+        // field offset is adjusted by -3 to account for chrom, chromStart, chromEnd columns
+        return ret.filter(f => {
+            if (!f.rest) {
+                return false;
+            }
+            const fieldIndex = (f.field || 0) - 3;
+            return getTabField(f.rest, fieldIndex) === name;
+        });
     }
 }
 exports.BigBed = BigBed;